Files in stianlagstad/chimeraviz
Visualization tools for gene fusions
.Rbuildignore
.gitignore
.lintr
.travis.yml
DESCRIPTION
ISSUE_TEMPLATE.md
NAMESPACE
NEWS
R/AllClasses.R
R/chimeraviz.R
R/extdata.R
R/get_fusion_by.R
R/import_aeron.R
R/import_chimpipe.R
R/import_defuse.R
R/import_ericscript.R
R/import_fusioncatcher.R
R/import_fusionmap.R
R/import_infusion.R
R/import_jaffa.R
R/import_oncofuse.R
R/import_prada.R
R/import_soapfuse.R
R/import_squid.R
R/import_starfusion.R
R/plot_circle.R
R/plot_fusion.R
R/plot_fusion_reads.R
R/plot_fusion_transcript.R
R/plot_fusion_transcript_with_protein_domain.R
R/plot_fusion_transcripts_graph.R
R/plot_transcripts.R
R/reports.R
R/utilities.R
README.md
chimeraviz.Rproj
docker/Dockerfile.devel
docker/Dockerfile.release
docker/README.md
environment.yml
fusion-plot-reduced.png
fusion-plot.png
fusion-reads-plot.png
fusion-transcript-graph-plot.png
fusion-transcript-plot-with-protein-domain-annotations.png
fusion-transcript-plot.png
fusion-transcripts-plot.png
inst/NEWS
inst/extdata/5267readsAligned.bam
inst/extdata/5267readsAligned.bam.bai
inst/extdata/FusionMap_01_TestDataset_InputFastq.FusionReport.txt
inst/extdata/Homo_sapiens.GRCh37.74.sqlite
inst/extdata/Homo_sapiens.GRCh37.74_subset.gtf
inst/extdata/PRADA.acc.fusion.fq.TAF.tsv
inst/extdata/UCSC.HG19.Human.CytoBandIdeogram.txt
inst/extdata/UCSC.HG38.Human.CytoBandIdeogram.txt
inst/extdata/UCSC.MM10.Mus.musculus.CytoBandIdeogram.txt
inst/extdata/aeron_fusion_support.txt
inst/extdata/aeron_fusion_transcripts.fa
inst/extdata/chimericJunctions_MCF-7.txt
inst/extdata/defuse_833ke_results.filtered.tsv
inst/extdata/ericscript_SRR1657556.results.total.tsv
inst/extdata/fusion5267and11759reads.bam
inst/extdata/fusion5267and11759reads.bam.bai
inst/extdata/fusion5267and11759reads.bedGraph
inst/extdata/fusioncatcher_833ke_final-list-candidate-fusion-genes.txt
inst/extdata/infusion_fusions.txt
inst/extdata/jaffa_results.csv
inst/extdata/oncofuse.outfile
inst/extdata/protein_domains_5267.bed
inst/extdata/reads.1.fq
inst/extdata/reads.2.fq
inst/extdata/reads_supporting_defuse_fusion_5267.1.fq
inst/extdata/reads_supporting_defuse_fusion_5267.2.fq
inst/extdata/soapfuse_833ke_final.Fusion.specific.for.genes
inst/extdata/squid_hcc1954_sv.txt
inst/extdata/star-fusion.fusion_candidates.final.abridged.txt
inst/extdata/star-fusion.fusion_predictions.abridged.annotated.coding_effect.tsv
inst/reports/fusionListReport.Rmd
inst/scripts/bowtie.R
inst/scripts/rsubread.R
man/Fusion-class.Rd
man/PartnerGene-class.Rd
man/add_fusion_reads_alignment.Rd
man/chimeraviz-internals-fusions_to_gene_label_data.Rd
man/chimeraviz-internals-fusions_to_link_data.Rd
man/chimeraviz-internals-scaleListToInterval.Rd
man/chimeraviz.Rd
man/create_fusion_report.Rd
man/decide_transcript_category.Rd
man/down_shift.Rd
man/downstream_partner_gene.Rd
man/fetch_reads_from_fastq.Rd
man/fusion_spanning_reads_count.Rd
man/fusion_split_reads_count.Rd
man/fusion_to_data_frame.Rd
man/get_ensembl_ids.Rd
man/get_fusion_by_chromosome.Rd
man/get_fusion_by_gene_name.Rd
man/get_fusion_by_id.Rd
man/get_transcripts_ensembl_db.Rd
man/import_aeron.Rd
man/import_chimpipe.Rd
man/import_defuse.Rd
man/import_ericscript.Rd
man/import_function_non_ucsc.Rd
man/import_fusioncatcher.Rd
man/import_fusionmap.Rd
man/import_infusion.Rd
man/import_jaffa.Rd
man/import_oncofuse.Rd
man/import_prada.Rd
man/import_soapfuse.Rd
man/import_squid.Rd
man/import_starfusion.Rd
man/partner_gene_ensembl_id.Rd
man/partner_gene_junction_sequence.Rd
man/plot_circle.Rd
man/plot_fusion.Rd
man/plot_fusion_reads.Rd
man/plot_fusion_transcript.Rd
man/plot_fusion_transcript_with_protein_domain.Rd
man/plot_fusion_transcripts_graph.Rd
man/plot_transcripts.Rd
man/raw_Homo_sapiens.GRCh37.74.Rd
man/raw_chimpipe.Rd
man/raw_cytobandhg19.Rd
man/raw_cytobandhg38.Rd
man/raw_defuse.Rd
man/raw_ericscript.Rd
man/raw_fusion5267proteindomains.Rd
man/raw_fusion5267reads.Rd
man/raw_fusion5267readsBedGraph.Rd
man/raw_fusioncatcher.Rd
man/raw_fusionmap.Rd
man/raw_infusion.Rd
man/raw_jaffa.Rd
man/raw_oncofuse.Rd
man/raw_prada.Rd
man/raw_soapfuse.Rd
man/raw_starfusion.Rd
man/select_transcript.Rd
man/show-Fusion-method.Rd
man/show-PartnerGene-method.Rd
man/split_on_utr_and_add_feature.Rd
man/upstream_partner_gene.Rd
man/write_fusion_reference.Rd
overview-plot.png
tests/testthat.R
tests/testthat/test_create_fusion_report.R
tests/testthat/test_fusions_to_gene_label_data.R
tests/testthat/test_fusions_to_link_data.R
tests/testthat/test_get_fusion_by.R
tests/testthat/test_import_aeron.R
tests/testthat/test_import_chimpipe.R
tests/testthat/test_import_defuse.R
tests/testthat/test_import_ericscript.R
tests/testthat/test_import_fusioncatcher.R
tests/testthat/test_import_fusionmap.R
tests/testthat/test_import_infusion.R
tests/testthat/test_import_jaffa.R
tests/testthat/test_import_oncofuse.R
tests/testthat/test_import_prada.R
tests/testthat/test_import_soapfuse.R
tests/testthat/test_import_squid.R
tests/testthat/test_import_starfusion.R
tests/testthat/test_import_starfusion2.R
tests/testthat/test_lintr.R
tests/testthat/test_plot_circle.R
tests/testthat/test_plot_fusion.R
tests/testthat/test_plot_fusion_reads.R
tests/testthat/test_plot_fusion_transcript.R
tests/testthat/test_plot_fusion_transcript_with_protein_domain.R
tests/testthat/test_plot_fusion_transcripts_graph.R
tests/testthat/test_plot_transcripts.R
tests/testthat/test_scale_list_to_interval.R
tests/testthat/test_select_transcript.R
tests/testthat/test_utilities.R
vignettes/chimeraviz-vignette.Rmd
